Factor Analysis with Correlated Topic Model for Multi-Modal Data

Integrating various data modalities brings valuable insights into underlying phenomena. Multimodal factor analysis (FA) uncovers shared axes of variation underlying different simple data modalities, where each sample is represented by a vector of features. However, FA is not suited for structured data modalities, such as text or single cell sequencing data, where multiple data points are measured per each sample and exhibit a clustering structure. To overcome this challenge, we introduce FACTM, a novel, multi-view and multi-structure Bayesian model that combines FA with correlated topic modeling and is optimized using variational inference. Additionally, we introduce a method for rotating latent factors to enhance interpretability with respect to binary features. On text and video benchmarks as well as real-world music and COVID-19 datasets, we demonstrate that FACTM outperforms other methods in identifying clusters in structured data, and integrating them with simple modalities via the inference of shared, interpretable factors.

Targeted AMP generation through controlled diffusion with efficient embeddings

Deep learning-based antimicrobial peptide (AMP) discovery faces critical challenges such as low experimental hit rates as well as the need for nuanced controllability and efficient modeling of peptide properties. To address these challenges, we introduce OmegAMP, a framework that leverages a diffusion-based generative model with efficient low-dimensional embeddings, precise controllability mechanisms, and novel classifiers with drastically reduced false positive rates for candidate filtering. OmegAMP enables the targeted generation of AMPs with specific physicochemical properties, activity profiles, and species-specific effectiveness. Moreover, it maximizes sample diversity while ensuring faithfulness to the underlying data distribution during generation. We demonstrate that OmegAMP achieves state-of-the-art performance across all stages of the AMP discovery pipeline, significantly advancing the potential of computational frameworks in combating antimicrobial resistance.

Unified Molecule Generation and Property Prediction

Modeling the joint distribution of the data samples and their properties allows to construct a single model for both data generation and property prediction, with synergistic capabilities reaching beyond purely generative or predictive models. However, training joint models presents daunting architectural and optimization challenges. Here, we propose Hyformer, a transformer-based joint model that successfully blends the generative and predictive functionalities, using an alternating attention mask together with a unified pre-training scheme. We show that Hyformer rivals other joint models, as well as state-of-the-art molecule generation and property prediction models. Additionally, we show the benefits of joint modeling in downstream tasks of molecular representation learning, hit identification and antimicrobial peptide design.

De Novo Drug Design with Joint Transformers

De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines a Transformer decoder, a Transformer encoder, and a predictor in a joint generative model with shared weights. We show that training the model with a penalized log-likelihood objective results in state-of-the-art performance in molecule generation, while decreasing the prediction error on newly sampled molecules, as compared to a fine-tuned decoder-only Transformer, by 42%. Finally, we propose a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties, as compared to the training data, outperforming other SMILES-based optimization methods in de novo drug design.

Artificial intelligence-driven antimicrobial peptide discovery

Antimicrobial peptides (AMPs) emerge as promising agents against antimicrobial resistance, providing an alternative to conventional antibiotics. Artificial intelligence (AI) revolutionized AMP discovery through both discrimination and generation approaches. The discriminators aid the identification of promising candidates by predicting key peptide properties such as activity and toxicity, while the generators learn the distribution over peptides and enable sampling novel AMP candidates, either de novo, or as analogues of a prototype peptide. Moreover, the controlled generation of AMPs with desired properties is achieved by discriminator-guided filtering, positive-only learning, latent space sampling, as well as conditional and optimized generation. Here we review recent achievements in AI-driven AMP discovery, highlighting the most exciting directions.

A generative recommender system with GMM prior for cancer drug generation and sensitivity prediction

Recent emergence of high-throughput drug screening assays sparkled an intensive development of machine learning methods, including models for prediction of sensitivity of cancer cell lines to anti-cancer drugs, as well as methods for generation of potential drug candidates. However, a concept of generation of compounds with specific properties and simultaneous modeling of their efficacy against cancer cell lines has not been comprehensively explored. To address this need, we present VADEERS, a Variational Autoencoder-based Drug Efficacy Estimation Recommender System. The generation of compounds is performed by a novel variational autoencoder with a semi-supervised Gaussian Mixture Model (GMM) prior. The prior defines a clustering in the latent space, where the clusters are associated with specific drug properties. In addition, VADEERS is equipped with a cell line autoencoder and a sensitivity prediction network. The model combines data for SMILES string representations of anti-cancer drugs, their inhibition profiles against a panel of protein kinases, cell lines biological features and measurements of the sensitivity of the cell lines to the drugs. The evaluated variants of VADEERS achieve a high r=0.87 Pearson correlation between true and predicted drug sensitivity estimates. We train the GMM prior in such a way that the clusters in the latent space correspond to a pre-computed clustering of the drugs by their inhibitory profiles. We show that the learned latent representations and new generated data points accurately reflect the given clustering. In summary, VADEERS offers a comprehensive model of drugs and cell lines properties and relationships between them, as well as a guided generation of novel compounds.